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root/gclib/tophat_cpp/fragments.h
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# Line 18 | Line 18
18   {
19    FragmentAlignmentGrade()
20    {
21 <    edit_dist = 0;
21 >    //edit_dist = 0;
22      num_alignments = 0;
23      status = AlignStatus();
24    }
# Line 26 | Line 26
26    FragmentAlignmentGrade(const BowtieHit& h1, const JunctionSet& gtf_junctions)
27    {
28      status = AlignStatus(h1, gtf_junctions);
29 <    edit_dist = h1.edit_dist();
29 >    //edit_dist = h1.edit_dist();
30      num_alignments = 1;
31    }
32    
33    FragmentAlignmentGrade& operator=(const FragmentAlignmentGrade& rhs)
34    {
35      status = rhs.status;
36 <    edit_dist = rhs.edit_dist;
36 >    //edit_dist = rhs.edit_dist;
37      num_alignments = rhs.num_alignments;
38      
39      return *this;
# Line 44 | Line 44
44      
45    bool operator<(const FragmentAlignmentGrade& rhs)
46    {
47 <    if (status != rhs.status)
47 >    // -- Geo: check this
48 >    //if (status != rhs.status)
49        return status < rhs.status;
50      
51 <    return rhs.edit_dist < edit_dist;
51 >    //return rhs.edit_dist < edit_dist;
52    }
53    
54    AlignStatus status;
55 <  int edit_dist;
55 >  //int edit_dist;
56    int num_alignments; // number of equally good alignments for this fragment
57   };
58  

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